Molecular Dynamics Simulations of the DNA-CNT Interaction Process: Hybrid Quantum Chemistry Potential and Classical Trajectory Approach
Affiliation(s)
1Tajik Technical University Named after M.S. Osimi, Dushanbe, Tajikistan 2Moscow State University of Technology “STANKIN”, Moscow, Russia. 1Institute of Nuclear Physics, Tashkent, Uzbekistan 2Laboratory of Radiation Biology, JINR, Dubna, Moscow Region, Russia. 1Moscow State University of Technology “STANKIN”, Moscow, Russia 2Laboratory of Radiation Biology, JINR, Dubna, Moscow Region, Russia 3Dubna International University, Dubna, Moscow Region, Russia.
1Tajik Technical University Named after M.S. Osimi, Dushanbe, Tajikistan 2Moscow State University of Technology “STANKIN”, Moscow, Russia. 1Institute of Nuclear Physics, Tashkent, Uzbekistan 2Laboratory of Radiation Biology, JINR, Dubna, Moscow Region, Russia. 1Moscow State University of Technology “STANKIN”, Moscow, Russia 2Laboratory of Radiation Biology, JINR, Dubna, Moscow Region, Russia 3Dubna International University, Dubna, Moscow Region, Russia.
ABSTRACT
In this work the quantum chemistry Tersoff potential in combination with classical trajectory calculations was used to investigate the interaction of the DNA molecule with a carbon nanotube (CNT). The so-called hybrid approach—the classical and quantum-chemical modeling, where the force fields and interaction between particles are based on a definite (but not unique) description method, has been outlined in some detail. In such approach the molecules are described as a set of spheres and springs, thereby the spheres imitate classical particles and the spring the interaction force fields provided by quantum chemistry laws. The Tersoff potential in hybrid molecular dynamics (MD) simulations correctly describes the nature of covalent bonding. The aim of the present work was to estimate the dynamical and structural behavior of the DNA-CNT system at ambient temperature conditions. The dynamical configurations were built up for the DNA molecule interacting with the CNT. The analysis of generated МD configurations for the DNA-CNT complex was carried out. For the DNA-CNT system the observations reveal an encapsulation-like behavior of the DNA chain inside the CNT chain. The discussions were made on possible use of the DNA-CNT complex as a candidate material in drug delivery and related systems.
Cite this paper
Khusenov, M. , Dushanov, E. and Kholmurodov, K. (2014) Molecular Dynamics Simulations of the DNA-CNT Interaction Process: Hybrid Quantum Chemistry Potential and Classical Trajectory Approach. Journal of Modern Physics, 5, 137-144. doi: 10.4236/jmp.2014.54023.
Khusenov, M. , Dushanov, E. and Kholmurodov, K. (2014) Molecular Dynamics Simulations of the DNA-CNT Interaction Process: Hybrid Quantum Chemistry Potential and Classical Trajectory Approach. Journal of Modern Physics, 5, 137-144. doi: 10.4236/jmp.2014.54023.
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http://dx.doi.org/10.1016/0263-7855(96)00018-5
[1] D. S. D. Larsson, Y. Wang and D. van der Spoel, Biochemistry, Vol. 48, 2009, pp. 1006-1015.
http://dx.doi.org/10.1021/bi801952f [2] E. G. Marklund, D. S. D. Larsson, D. van der Spoel, A. Patriksson and C. Caleman, Physical Chemistry Chemical Physics, Vol. 11, 2009, pp. 8069-8078.
http://dx.doi.org/10.1039/b903846a [3] R. Friemann, D. S. D. Larsson, Y. Wang and D. van der Spoel, Journal of the American Chemical Society, Vol. 131, 2009, pp. 16606-16607.
http://dx.doi.org/10.1021/ja902962y [4] D. van der Spoel, E. Marklund, D. S. D. Larsson and C. Caleman, Macromolecular Bioscience, Vol. 11, 2011, pp. 50-59. http://dx.doi.org/10.1002/mabi.201000291 [5] Kh. Kholmurodov, “Molecular Simulation Studies in Material and Biological Sciences,” Nova Science Publishers Ltd., 2007, 196 p. [6] Kh. Kholmurodov, “Molecular Simulation in Material and Biological Research,” Nova Science Publishers Ltd., 2009, 155 p. [7] Kh. Kholmurodov, “Molecular Dynamics of Nanobistructures,” Nova Science Publishers Ltd., 2011, 210 p. [8] Kh. Kholmurodov, “Models in Bioscience and Materials Research: Molecular Dynamics and Related Techniques,” Book of International Workshop MSSMBS’12, Nova Science Publishers Ltd., 2013, 208 p. [9] J. Santa Lucia Jr. and D. Hicks, Annual Review of Biophysics and Biomolecular Structure, Vol. 33, 2004, pp. 415-440.
http://dx.doi.org/10.1146/annurev.biophys.32.110601.141800 [10] K. J. Breslauert, R. Franks, H. Blockers and L. A. Markyt, Proceedings of the National Academy of Sciences of the United States of America, Vol. 83, 1986, pp. 3746-3750.
http://dx.doi.org/10.1073/pnas.83.11.3746 [11] V. Freyre-Fonseca, et al., Toxicology Letters, Vol. 202, 2011, pp. 111-119.
http://dx.doi.org/10.1016/j.toxlet.2011.01.025 [12] B. Trouiller, R. Reliene, A. Westbrook, P. Solaimani and R. H. Schiestl, Cancer Research, Vol. 69, 2009, pp. 8784-8789. http://dx.doi.org/10.1158/0008-5472.CAN-09-2496 [13] Q. Saquib, A. A. Al-Khedhairy, M. A. Siddiqui, F. M. Abou-Tarboush, A. Azam and J. Musarrat, Toxicology in Vitro, Vol. 26, 2012, pp. 351-361.
http://dx.doi.org/10.1016/j.tiv.2011.12.011 [14] R. Dunford, A. Salinaro, L. Cai, N. Serpone, S. Horikoshi, H. Hidaka and J. Knowland, FEBS Letters, Vol. 418, 1997, pp. 87-90.
http://dx.doi.org/10.1016/S0014-5793(97)01356-2 [15] C. Srinivasan, Current Science, Vol. 94, 2008, pp. 300-301. [16] T. A. Hilder and J. M. Hill, Current Applied Physics, Vol. 8, 2008, pp. 258-261.
http://dx.doi.org/10.1016/j.cap.2007.10.011 [17] T. A. Hilder and J. M. Hill, Micro & Nano Letters, Vol. 3, 2008, pp. 41-49. http://dx.doi.org/10.1049/mnl:20080008 [18] Q. Chen, Q. Wang, Y. C. Liu, T. Wu, Y. Kang, J. D. Moore and K. G. Gubbins, Journal of Chemical Physics, Vol. 131, 2009, Article ID: 015101. [19] I. Ali, D. Marenduzzo and J. M. Yeomans, Physical Review Letters, Vol. 96, 2006, Article ID: 208102.
http://dx.doi.org/10.1103/PhysRevLett.96.208102 [20] I. Ali, D. Marenduzzo and J. M. Yeomans, Biophysical Journal, Vol. 94, 2008, pp. 4159-4164.
http://dx.doi.org/10.1529/biophysj.107.111963 [21] J. V. Veetil and K. Ye, Biotechnology Progress, Vol. 23, 2007, pp. 517-531. http://dx.doi.org/10.1021/bp0602395 [22] S. Dhar, Z. Liu, J. Thomale, H. J. Dai and S. J. Lippard, Journal of the American Chemical Society, Vol. 130, 2008, pp. 11467-11476.
http://dx.doi.org/10.1021/ja803036e [23] J. Tersoff, Physical Review B, Vol. 39, 1989, pp. 5566-5568. http://dx.doi.org/10.1103/PhysRevB.39.5566 [24] Kh. Kholmurodov, G. Aru and K. Yasuoka, Natural Science, Vol. 2, 2010, pp. 902-910.
http://dx.doi.org/10.4236/ns.2010.28111 [25] Kh. Kholmurodov, et al., Chemical Physics, Vol. 402, 2012, pp. 41-47.
http://dx.doi.org/10.1016/j.chemphys.2012.04.002 [26] K. A. Affholter, S. J. Henderson, G. D. Wignall, G. J. Bunick, R. E. Haufler and R. N. Compton, The Journal of Chemical Physics, Vol. 99, 1993, pp. 9224-9229.
http://dx.doi.org/10.1063/1.465538 [27] Y. B. Melnichenko, G. D. Wignall, R. N. Compton and G. Bakale, The Journal of Chemical Physics, Vol. 111, 1999, pp. 4724-4728. http://dx.doi.org/10.1063/1.479234 [28] H. E. Smorenburg, R. M. Crevecoeur, I. M. de Schepper and L. A. de Graaf, Physical Review E, Vol. 52, 1995, pp. 2742-2752. http://dx.doi.org/10.1103/PhysRevE.52.2742 [29] F. Migliardo, V. Magazù and M. Migliardo, Journal of Molecular Liquids, Vol. 10, 2004, pp. 3-6.
http://dx.doi.org/10.1016/j.molliq.2003.08.010 [30] T. Tomiyama, S. Uchiyama and H. Shinohara, Chemical Physics Letters, Vol. 264, 1997, pp. 143-148.
http://dx.doi.org/10.1016/S0009-2614(96)01290-0 [31] A. D. Bokare and A. Patnaik, Journal of Chemical Physics, Vol. 119, 2003, pp. 4529-4538.
http://dx.doi.org/10.1063/1.1594177 [32] W. Smith and T. R. Forester, Journal of Molecular Graphics, Vol. 14, 1996, pp. 136-141.
http://dx.doi.org/10.1016/S0263-7855(96)00043-4 [33] W. Smith, T. R. Forester and I. T. Todorov, “The DL_POLY 2 User Manual,” STFC Daresbury Laboratory Daresbury, Warrington WA4 4AD Cheshire, UK, Version 2.19, 2008. [34] Y. Kang, Y. C. Liu, Q. Wang, T. Wu and W. J. Guan, Biomaterials, Vol. 30, 2009, pp. 2807-2815.
http://dx.doi.org/10.1016/j.biomaterials.2009.01.024 [35] Y. H. Xie and A. K. Soh, Materials Letters, Vol. 59, 2005, pp. 971-975.
http://dx.doi.org/10.1016/j.matlet.2004.10.079 [36] D. S. D. Larsson, L. Liljas and D. van der Spoel, PLOS Computational Biology, Vol. 8, 2012, Article ID: e100 2502. http://dx.doi.org/10.1371/journal.pcbi.1002502 [37] B.-D. Chen, C.-L. Yang, M.-S. Wang and X.-G. Ma, Chinese Physics B, Vol. 21, 2012, Article ID: 083103. [38] W. Humphrey, A. Dalke and K. Schulten, Journal of Molecular Graphics, Vol. 14, 1996, pp. 33-38.
http://dx.doi.org/10.1016/0263-7855(96)00018-5